Mercurial > repos > galaxyp > openms
view IDFileConverter.xml @ 3:75537a09e9fa draft
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author | bgruening |
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date | Wed, 13 May 2015 18:33:49 -0400 |
parents | 3070d71e0e5c |
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<?xml version='1.0' encoding='UTF-8'?> <tool id="IDFileConverter" name="IDFileConverter" version="2.0.0"> <description>Converts identification engine file formats.</description> <macros> <token name="@EXECUTABLE@">IDFileConverter</token> <import>macros.xml</import> </macros> <expand macro="stdio"/> <expand macro="requirements"/> <command>IDFileConverter #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_out_type: -out_type #if " " in str($param_out_type): "$param_out_type" #else $param_out_type #end if #end if #if $param_mz_file: -mz_file $param_mz_file #end if #if $param_mz_name: -mz_name "$param_mz_name" #end if #if $param_use_precursor_data: -use_precursor_data #end if #if $param_peptideprophet_analyzed: -peptideprophet_analyzed #end if -threads \${GALAXY_SLOTS:-24} #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_ignore_proteins_per_peptide: -ignore_proteins_per_peptide #end if #if $adv_opts.param_scan_regex: -scan_regex "$adv_opts.param_scan_regex" #end if #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param name="param_in" type="data" format="xml,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific XML format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml), <br>- for Sequest results, a directory containing .out files. <br>"/> <param name="param_out_type" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) "> <option value="idXML">idXML</option> <option value="mzid">mzid</option> <option value="pepXML">pepXML</option> <option value="FASTA">FASTA</option> </param> <param name="param_mz_file" type="data" format="mzxml,mzml" optional="True" label="[Sequest, pepXML, mascotXML, XTandem only] Retention times will be looked up in this file" help="(-mz_file) "/> <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_use_precursor_data" type="boolean" truevalue="-use_precursor_data" falsevalue="" checked="false" optional="True" label="[pepXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra" help="(-use_precursor_data) "/> <param name="param_peptideprophet_analyzed" type="boolean" truevalue="-peptideprophet_analyzed" falsevalue="" checked="false" optional="True" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="(-peptideprophet_analyzed) By default a 'raw' pepXML is produced that contains only search engine results"/> <expand macro="advanced_options"> <param name="param_ignore_proteins_per_peptide" type="boolean" truevalue="-ignore_proteins_per_peptide" falsevalue="" checked="false" optional="True" label="[Sequest only] Workaround to deal with .out files that contain" help="(-ignore_proteins_per_peptide) e.g. "+1" in references column, <br>but do not list extra references in subsequent lines (try -debug 3 or 4)"/> <param name="param_scan_regex" type="text" size="30" label="[mascotXML only] Regular expression used to extract the scan number or retention time" help="(-scan_regex) See documentation for details"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs> <outputs> <data name="param_out" format="fasta"/> </outputs> <help>**What it does** Converts identification engine file formats. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help> <expand macro="references"/> </tool>